Forschungsprojekte

Current projects
 

AnnoSys II – A Generic Annotation System for Biodiversity Data

The project develops strategies and software for bringing traditional annotation workflows for biodiversity data to the Internet. Traditionally, experts add information to biological specimens in written form. These annotation labels are stored with the specimen and provide an important quality control mechanism and improve the value of herbarium.
 
During its first phase, the project developed a fully functional prototype of an annotation data repository for complex and cross-linked data including back-end server functionality, web services and an on-line user interface. Main objectives of the current project phase are (1) rolling out the software to major biodiversity portals in order to further establish the system and methodology in the domain and to gather user input for improving the interface and procedures. This will include extensions of the types of biodiversity content handled by the system and (2) extending the generic qualities of AnnoSys to further structured data formats including non-XML-based standards with machine readable explicit semantic concepts, and thus opening up the data gathered through AnnoSys for the Semantic Web and Open Data. This will also include the investigation and integration with other annotation systems based on the W3 Open Annotation Community Group standard.
 
The 3-year project (2015-2017) is funded by the LIS-Programme of the German Research Foundation (DFG).
 

A community platform for the development and documentation of the ABCD standard for natural history collections

The project ABCD (Access to Biological Collection Data) is an international standard for the exchange of biological collection and observation data. Development started in 2001; in 2005 it was ratified as an XML schema as TDWG standard (Biodiversity Information Standards). From the outset the ABCD development was based on an XML schema and the documentation of the individual concepts is represented as XML annotations. New ABCD-versions are created periodically by consolidating and integrating user requirements collected by the coordination team at the BGBM. This method was effective in the first decade of the ABCD development. However, due to a growing and diversifying user community and the introduction of semantic technologies it is reaching certain limits. The ABCD concepts are arranged hierarchically and are referenced by their xpath from the root node. A direct use in the Semantic Web is therefore not possible. The proposed project aims to develop a platform that provides ABCD concepts in a machine-readable form, together with a versioned documentation. The dependency of the ABCD concepts from an XML schema will be resolved and the concepts will be provided as an ontology for the Semantic Web. The version 3.0 of the ABCD standards will include the concepts developed by various domain specific extensions and will be made available both as an XML schema and as an ontology in the Semantic Web.
 
The 3-year project (2014-2017) is funded by the LIS-programme of the German Research Foundation (DFG).
 

EU BON – Building the European Biodiversity Observation Network (link is external)

EU BON is to build a substantial part of the Group on Earth Observation’s Biodiversity Observation Network (GEO BON). EU BON’s deliverables include a comprehensive "European Biodiversity Portal" for all stakeholder communities, and strategies for a global implementation of GEO BON and supporting IPBES. Due to EU BON’s contribution overall European capacities and infrastructures for environmental information management will be strengthened.
The BGBM will provide a harmonized taxonomic backbone for the EU BON infrastructure and contribute to the mobilisation of specimen data. The 5-year project (2012 - 2017) is funded under the EU’s 7th Framework Programme. 

 

Europeana Digital Service Infrastructure (DSI)

www.Europeana.eu is the cross-domain central portal to Europe’s digitized cultural and scientific heritage. The portal links to almost 50 million of digital objects from Europe’s museums, galleries, archives, libraries and audio-visual collections. Europeana’s vision is to make cultural heritage as easily accessible and as freely reusable as possible. The Europeana DSI project aims to ensure the continued operation of the Europeana Digital Service Infrastructure (DSI) and to facilitate the transition of the Europeana website from a portal to a multi-sided platform, offering a variety of services to data providers, end users and re-users. The Freie Universität Berlin on behalf the OpenUp! network is involved in Work Package 1 focussing on the innovation of the aggregation infrastructure. Key objectives are to make it easier for providers to add their content to the Europeana site; improve the quality of metadata and the quantity of digital objects available; and increase the amount of objects with open licencing conditions.
 
OpenUp! is a growing network of European institutions providing natural history objects to Europeana. This includes digitized specimens, natural history artwork, animal sounds, and videos. The OpenUp! natural history aggregator for Europeana is coordinated by the Freie Universität Berlin, Botanic Garden und Botanical Museum Berlin-Dahlem (BGBM). Collections provide standardised metadata via the BioCASe Provider Software (Biological Collection Access Service) or the GBIF Integrated Publishing Toolkit (IPT), feeding into the aggregation process that includes the harvest, transformation and transfer of metadata to Europeana. During the process scientific metadata items are enriched by literature references, geo names, and common names of plants and animals to increase the accessibility of objects by non-scientific users. So far, 23 partners from 12 European countries take part in the OpenUp! network and contribute 2.2 million records. Data providers benefit from reaching new audiences, increasing web traffic to institutional websites and gaining better visibility towards research funding organizations and within society.
 
The Europeana DSI project is funded 2015-2016 and 2016-2017 under the Connecting Europe Facility (CEF) that supports trans-European networks and infrastructures in the sectors of transport, telecommunications and energy.
 

GBIF Edaphobase - Informationssystem, Daten-Repositorium, Daten-Infrastruktur und Service-Plattform für die Bodenzoologie 

The project develops a soil zoology information system with comprehensive ecological and taxonomic query mechanisms. The system serves as a publicly available tool for biodiversity sciences and give access to distributed collection data as well as data from literature.
 
The BGBM supports the integration of Edaphobase in the infrastructure of GBIF-Germany and supports the setup of a taxonomic backbone system based on the EDIT Platform for Cybertaxonomy. The 4-year project (2013 - 2017) is funded by the Federal Ministry of Education and Research.
 

German Federation of Biological Data (GFBio) – Phase II

Environmental and biological research is becoming central to major societal challenges related to the Earth’s ecosystems and climate dynamics. To handle the scale and complexity of the scientific questions being addressed, there is a strong need to integrate knowledge because biological data are currently scattered and difficult to share. We propose here a coherent infrastructure to improve scientific data integration and preservation.
 
The project brings together national key players providing environmentally related biological data and services to develop the ‘German Federation of Biological Data’ (GFBio). The overall goal is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research. The federation will build on proven data archiving infrastructures and workflows such as those of PANGAEA for environmental data and the resources of Germany's major natural history collection data repositories. The new infrastructure will improve and integrate these existing components within a common technological and organizational framework.
 
The planned infrastructure will address data management requirements of a large range of stakeholders including individual scientists, natural history collections as well as larger research networks. It will be capable to handle highly interdisciplinary heterogeneous data. Within the current project, special consideration will be given to genome data, ecological and environmental data as well as collection related data. Services provided by the GFBio will cover the full life cycle of research data from field or real time data acquisition to long term archiving and publication as well as analysis and re-use of these data.
 
The BGBM leads work package 7 (Networking and Interoperability). An important aspect is the provision of terminology services supporting semantic enrichment and integration of research data.
 
GFBio II (2015 - 2018) is funded by the German research Foundation (DFG).
 

Die Herbonauten - Pilot Study

The project will setup a web-based system as a pilot study supporting the transcription of digitised herbarium label information by citizen scientists. The system will use well established software developed by the Paris Natural History Museum (Les herbonautes).
 
The project is funded by the Friends of the Botanic Garden and Botanical Museum Berlin.
 

Herbadrop: an innovative approach to long-term analysis of digitised herbarium specimens.

The project will offer an archival service for long-term preservation of herbarium specimen images and develop software-driven innovative processes for extracting metadata from those images.
 
The BGBM provides high-quality digitised herbarium specimens and contributes to the specification of workflows and data formats.
 
The 18 months project (2016 – 2017) is funded by the EUDAT data pilot programme.
 

RL2020: Kooperation Checklisten

Red Lists of animals, plants and fungi are scientific reports documenting the actual level of threat for endangered species in a certain area. The German Red Lists are comprehensive species lists (including non-threatened organisms) published by the Federal Agency for Nature Conservation (BfN, Bonn) and updated every 10 years. The project aims to renew the Red List preparation process in order to facilitate the long-time collaboration of scientists, federal and regional authorities as well as contributing citizens and volunteers interested in nature conservation. The project will test and deploy a software infrastructure designed during the preparation phase project “Rote Listen 2020 - Vorbereitungsphase”.
 
The 3-year project (2015 - 2018) is funded by the German Federal Agency for Nature Conservation (Bundesamt für Naturschutz, BfN).
 

SYNTHESYS, SYNTHESYS-2 and SYNTHESYS-3

SYNTHESYS aims at consolidating the Information Network of European Natural History Collections.
In the first SYNTHESYS project, the Networking Activity D (NA D), coordinated by BGBM, established the basic, core mechanisms for sharing and working with existing datasets held within infrastructures. Standards and protocols were developed (e.g. ABCDEFG schema for specimen-based earth science collection data) to ensure standardised access to collection data via the specifically designed interfaces (e.g. SYNTHESYS BioCASE Portal).
 
In the current succeeding project, BGBM coordinates Networking Activity 3 (NA3), which aims at removing barriers to the electronic access and sharing of collections information by providing the state-of-the-art tools for specialist Users and improving the quality of content supplied by the global scientific community through implementation of best practice and the setting of global data standards. NA3 will ensure the integration of the SYNTHESYS IA Beneficiaries into the emerging virtual biodiversity information facilities on the European level.
In the third phase of SYNTHESYS (starting in 2013) the BGBM will coordinate the technical implementation of the DNA Bank Network in Europe. The BGBM also participates in the German Taxonomic Access Facility DE-TAF of SYNTHESYS.
 
The project is funded under the EU 7th Framework Programme of the European Community for Research, Technological Development and Demonstration, Infrastructures. Duration: 2009-2013, 2013-2017.
 

Expanding the “DNA Bank Network” into the “Global Genome Biodiversity Network”

In this project, the DNA Bank Network’s technologies and standards will be optimized and enhanced to serve as a technical solution on a global scale for the Global Genome Biodiversity Network (GGBN). By connecting the data of the Global Genome Initiative (GGI) of the Smithsonian National Museum of Natural History (Washington DC/USA) to the GGBN Data Portal all necessary ameliorations to the existing technical structures and solutions can be achieved to successively add all other GGBN partner institutions in the future. This implies for instance the revision of the GGBN Data Standard and its implementation within DwC-A as well as adding parts of the GBIF checklist bank as taxonomic backbone to the data portal. Furthermore, collaboration will also be tightened with international initiatives like GBIF, INSDC, ESBB, ISBER, SYNTHESYS, EDIT, GSC etc. to finally serve as a global platform for knowledge exchange concerning biodiversity tissue and DNA banking in general, which doesn’t exist so far.
 
The 2-year project (2014-2015) is funded by the German Research Foundation (DFG).
 

StanDAP-Herb: A standardised and optimised process for data acquisition from digital images of herbarium specimens

The project will develop and document a software-driven standard process for extracting metadata from images of herbarium specimens (i.e. dried pressed plants or plant parts mounted on cardboard and stored in natural history collections). We will address a large proportion of science collections: approximately 22 million herbarium specimens exist as botanical reference objects in Germany, about 500 million worldwide. Metadata like plant name, collection site and date, collector, accession numbers, etc. are also glued flat on the sheet and thus visible on the specimen image. Up to now most of the data capture is manually fed into collection databases, but increasingly, imaging techniques are employed (also to ensure that the on-line metadata can be verified). The standard process shall replace or add to the manual data input as much as possible. Image processing software detects objects on the digitized record and classifies them. Text objects will be transformed into structured information using text mining algorithms. For handwriting, author identification is attempted. The project will evaluate and enhance existing software to conform to standard interfaces and integrate it into an overall open software architecture on the basis of established IT standards. Finally, the requirements for the process will be formulated as a standard and the actual application will be documented.
 
The 3-year project (2014-2017) is funded by the LIS-programme of the German Research Foundation (DFG).
 

Permanent online resources

 

Coordination of the GBIF-D Node System and the Botanical Node

Germany is one of the founding nations of the Global Biodiversity Information Facility (GBIF). Main objective of the GBIF-D project is the focussed collection and mobilisation of suitable data within Germany's research community and natural history collections as well as of the available observation data.

The BGBM is coordinating this 6-partner project to ensure the technical and organisational cohesion of the eight Nodes in the German GBIF system:  

 

•             BGBM Berlin-Dahlem responsible for Coordination

•             DSMZ Braunschweig responsible for Bacteria & Archaea

•             BGBM Berlin-Dahlem responsible for Plants & Protists

•             BSM München responsible for Fungi & Lichens

•             MfN Berlin responsible for Insects

•             ZSM München responsible for Invertebrates II

•             Senckenberg Frankfurt responsible for Invertebrates III

•             ZFMK Bonn responsible for Vertebrates

•             MfN Berlin responsible for Fossils

 

The German Botanical Node of the Global Biodiversity Information Facility has been established at the BGBM in close collaboration with ten German botanical institutions and five other partner institutions as part of the German contribution to GBIF International. It represents all flowering plants, ferns, and mosses and also puts a special accent on algae and protists.The project at the BGBM supports the German botanical community in their efforts to mobilise botanical data using the BioCASE software and to create a German Virtual Herbarium.

 

OpenUp! - Opening up the European Natural History Heritage for EUROPEANA

The institutions participating in OpenUp! will provide over one million multimedia objects from the natural history domain to Europeana, the European Virtual Library (www.europeana.eu). OpenUp! is complementary to the eContentPlus project Biodiversity Heritage Library Europe, which mobilised digitised literature in the natural history domain. OpenUp! is an initiative of members of the Consortium of European Taxonomic Facilities (CETAF) and several European nodes of the Global Biodiversity Information Facility (GBIF).
The BGBM is responsible for the overall coordination of OpenUp! and provides high-quality herbarium images to the system. 

 

European Distributed Institute of Taxonomy - EDIT, Platform for Cybertaxonomy

The overall objective of EDIT was to integrate European taxonomic effort within the European Research Area and to build a world leading capacity. EDIT work-package 5 was lead by the BGBM and created the “Internet Platform for Cybertaxonomy”.

The EDIT Platform is an integrated software suite providing tools and support of the entire taxonomic workflow that leads to the creation of taxonomic monographs, checklists, flora and fauna treatments.
The software is further developed, promoted and sustained in the framework of several projects and as a core activity of the BGBM’s Biodiversity Informatics Research Group.

European Distributed Institute of Taxonomy – EDIT Cichorieae examplar group.

In the workpackage "Unifying revisionary taxonomy" of the EDIT project the BGBM created an exemplar site using the EDIT Platform for Cybertaxonomy. The Cichorieae network is sustained by the BGBM’s Asterales Research Group.

DNA Bank Network and Global Genome Biodiversity Network (GGBN)

The Botanic Garden and Botanical Museum Berlin-Dahlem is a founding member and the coordinator of the DNA Bank Network. The DNA Bank Network was established in spring 2007 and was funded until 2011 by the German Research Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility). It offers a worldwide unique concept based on GBIF and BioCASe. DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals).
In 2011 the Global Genome Biodiversity Network has been founded by the DNA Bank Network, as well as GBIF, Smithsonian Institution, Natural History Museum London, Natural History Museum Denmark and many others. At present more than 29 DNA and tissue banks are GGBN members. The existing data portal of the DNA Bank Network will serve as the data portal for GGBN in the near future. The aim is to provide all available samples from all GGBN partners via this central data portal and to build a knowledge platform on non-human biobanking.
The GGBN/DNA Bank Network data portal is further developed, promoted and sustained in the framework of other projects and as a core activity of the BGBM’s Biodiversity Informatics Research Group.


PESI /EU-Nomen

PESI stands for Pan-European Species directories Infrastructure. Authoritative species name registers are not only essential for taxonomy but important for information systems dealing with species of conservation, pest or commercial relevance as well. PESI enhances the quality and reliability of such European registers by integrating community networks of taxonomic experts into a joint work programme.
In the project (2008-2011, funded by the EU under FP7) the BGBM lead the integration of the European Register of Marine Species, Fauna Europaea and Euro+Med Plantbase into a joint information system. The joint PESI infrastructure is maintained with the partners as an activity of the BGBM’s Biodiversity Informatics Group and in projects such as EU-BON.


Digital specimen images at the Herbarium Berolinense (B)

Since 2004, high resolution digital camera equipment is used to produce digital images of herbarium specimens. The digitisation of type specimens and some of the important collections such as the Herbaria Willdenow and Bridel were and are funded by the Andrew W. Mellon foundation in the framework of the Global Plant Initiative.The German Virtual Herbarium is part of the GBIF-D project financed by the Federal Ministry of Research and Education, which also provided the funding for a large scale improvement of the underlying hardware in 2010. Contributing digitisation activities are also taking place as part of the BGBM’s loan system, and have been supported by the Association of Friends of the BGBM.


A Biological Collection Access Service for Europe: BioCASE

Originally a 35-partner research and development project co-ordinated by the BGBM, starting  Nov. 1, 2001 financed under the EU's 5th Framework Programme, Research Infrastructures until Jan. 31, 2005. Since then, the suit of software and activities in the area of has become one of . The BGBM is responsible for over-all co-ordination and for the development of the access system. The initiative is sustained in the framework of SYNTHESYS, GBIF-D and as a core activity of the BGBM’s Biodiversity Informatics Research Group.